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Intermediate analogue in benzoylformate decarboxylase
Analyse Intermediate analogue in benzoylformate decarboxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FZN
- Type
- protein
- Length
- 2,092 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzoylformate decarboxylase
- EC
- 4.1.1.7
- UniProt
- P20906
- Ligands
- D7K, MG, CL, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Benzoylformate decarboxylase (EC 4.1.1.7) | protein | 523 | 40% helix, 19% strand | P20906 |
Ligands and binding sites
- D7K · 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 11 copies · chains A, D, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, D, B, C
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.88 | 0.93 | 105 | CL |
| 2 | 473 | 0.86 | 0.93 | 89 | empty |
| 3 | 225 | 0.80 | 0.94 | 38 | empty |
| 4 | 662 | 0.78 | 0.83 | 78 | D7K, MG |
| 5 | 591 | 0.78 | 0.84 | 72 | D7K, MG |
Interfaces
6 interfaces between chains.
- A–B · 3619 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 3610 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1726 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1724 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 567 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P20906
- Elsewhere: RCSB PDB 3FZN · PDBe 3FZN · UniProt P20906
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